Background Intestinal protozoan infection is a public health problem in Indonesia, particularly in regions lacking clean water sources such as Perokonda and Perobatang villages, Southwest Sumba Regency, East Nusa Tenggara Province. The residents of Perokonda and Perobatang villages use wells and unprotected open springs respectively. Therefore, this study aims to determine the prevalence of intestinal protozoan infections in these two villages. Materials and Methods This was a cross-sectional study, carried out in Perokonda and Perobatang from August 2016 to August 2017. A total of 291 children aged 6 months to 18 years were used as subjects. Furthermore, fecal examinations were carried out by preparing smears, which were stained with lugol solution and examined under the microscopes by four experienced technicians. The data were processed using SPSS version 20 and analyzed by chi-square test. Results Among the 291 samples, the prevalence of intestinal protozoan infections was 20%, with 23.4% in Perokonda and 17.2% in Perobatang. The predominant species found were Blastocystis hominis (34.5%), Giardia lamblia (19.0%), and Entamoeba coli (15.5%). Moreover, approximately 69.0% of single infections were found while 31.0% were mixed and associated with 2 to 3 protozoan species. There were no significant differences between the prevalence of intestinal protozoan infections and the children in Perokonda and Perobatang villages (confidence interval 0.83 - 2.62, P = 0.19). Conclusion The type of water sources has no relationship with the species of intestinal protozoan infecting children in Perokonda and Perobatang.